Beta-hexosaminidase is a lysosomal enzyme composed of two polypeptide chains, encoded on different chromosomes and designated the alpha and beta chains. Mutations in the alpha-chain result in Tay-Sachs disease, an inherited disorder displaying clinical and biochemical heterogeneity. The classic form of the disease has a ten-fold higher gene frequency among Ashkenazi Jews than the general population. We have previously isolated a cDNA clone encoding a small fragment of the 3'-terminal of the alpha-chain mRNA. Using this clone as a probe, we showed a deficiency of alpha-chain mRNA Ashkenazi Tay-Sachs fibroblasts. During the past year we have continued this project and have isolated a nearly full-length cDNA clone for the alpha-chain of human beta-hexosaminidase. We determined the nucleotide sequence and derived amino acid sequence of the clone and found it to contain the entire coding sequences of the alpha-chain polypeptide. We found a striking sequence homology between the published sequence for two beta-chain peptides and the derived alpha-chain primary structure suggesting that both chains may have arisen from a common ancestor. In addition a second, larger and less abundant mRNA coding for the alpha-chain in human fibroblast cultures was characterized. It was found to differ from the smaller more abundant alpha-chain message by an extension at its 3'-end.